Multiple sequence alignment - TraesCS1A01G041700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G041700 chr1A 100.000 3451 0 0 1 3451 22754506 22757956 0.000000e+00 6373
1 TraesCS1A01G041700 chr1D 95.787 2872 103 10 3 2861 10937476 10934610 0.000000e+00 4617
2 TraesCS1A01G041700 chr1D 98.018 555 6 3 2902 3451 10934612 10934058 0.000000e+00 959
3 TraesCS1A01G041700 chr1B 90.827 1984 132 21 701 2658 16428592 16426633 0.000000e+00 2610
4 TraesCS1A01G041700 chr1B 88.786 758 61 14 1843 2578 39846899 39846144 0.000000e+00 907
5 TraesCS1A01G041700 chr1B 83.916 429 56 11 3027 3451 16425455 16425036 6.940000e-107 398
6 TraesCS1A01G041700 chr1B 83.645 428 59 10 3027 3451 39828445 39828026 3.230000e-105 392
7 TraesCS1A01G041700 chr1B 82.710 214 30 6 3239 3451 39821768 39821561 2.120000e-42 183
8 TraesCS1A01G041700 chr1B 94.318 88 5 0 615 702 16428834 16428747 6.010000e-28 135
9 TraesCS1A01G041700 chr7B 78.240 1443 265 36 1013 2434 551897345 551898759 0.000000e+00 880
10 TraesCS1A01G041700 chr7B 77.169 1441 284 35 1013 2434 551539069 551540483 0.000000e+00 797
11 TraesCS1A01G041700 chr7D 77.871 1428 274 31 1028 2437 518091059 518089656 0.000000e+00 848
12 TraesCS1A01G041700 chr7D 77.616 1443 272 39 1013 2434 518573745 518575157 0.000000e+00 828
13 TraesCS1A01G041700 chr7A 77.824 1434 266 34 1028 2437 593015991 593014586 0.000000e+00 839
14 TraesCS1A01G041700 chr7A 80.401 898 162 10 1544 2434 593376913 593377803 0.000000e+00 671
15 TraesCS1A01G041700 chr7A 78.118 457 79 15 1013 1463 593376389 593376830 1.580000e-68 270
16 TraesCS1A01G041700 chr7A 76.347 334 56 16 390 704 641742568 641742897 1.280000e-34 158
17 TraesCS1A01G041700 chrUn 83.977 518 51 13 3 514 27691980 27692471 5.220000e-128 468
18 TraesCS1A01G041700 chrUn 95.506 89 3 1 618 706 27692500 27692587 1.290000e-29 141
19 TraesCS1A01G041700 chr3A 90.686 204 17 2 4 206 40808537 40808739 1.580000e-68 270
20 TraesCS1A01G041700 chr3A 90.000 80 7 1 619 698 40810281 40810359 6.090000e-18 102
21 TraesCS1A01G041700 chr2D 81.726 197 31 5 384 576 567800704 567800509 3.560000e-35 159
22 TraesCS1A01G041700 chr2D 80.526 190 22 9 127 307 148961497 148961314 7.770000e-27 132
23 TraesCS1A01G041700 chr2D 87.273 110 14 0 2903 3012 41264071 41264180 3.620000e-25 126
24 TraesCS1A01G041700 chr5B 86.885 122 15 1 567 688 143502094 143502214 6.010000e-28 135
25 TraesCS1A01G041700 chr5B 84.615 130 17 2 2903 3030 462328918 462329046 3.620000e-25 126
26 TraesCS1A01G041700 chr5B 84.252 127 20 0 2904 3030 182472583 182472457 1.300000e-24 124
27 TraesCS1A01G041700 chr5A 85.156 128 18 1 2904 3031 676758956 676759082 2.800000e-26 130
28 TraesCS1A01G041700 chr5A 84.496 129 18 2 2903 3030 531690042 531690169 3.620000e-25 126
29 TraesCS1A01G041700 chr6A 88.462 104 12 0 2909 3012 96809458 96809355 3.620000e-25 126
30 TraesCS1A01G041700 chr2B 84.800 125 19 0 2903 3027 796371454 796371578 3.620000e-25 126
31 TraesCS1A01G041700 chr6B 82.031 128 23 0 2903 3030 714045345 714045472 3.640000e-20 110


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G041700 chr1A 22754506 22757956 3450 False 6373.000000 6373 100.0000 1 3451 1 chr1A.!!$F1 3450
1 TraesCS1A01G041700 chr1D 10934058 10937476 3418 True 2788.000000 4617 96.9025 3 3451 2 chr1D.!!$R1 3448
2 TraesCS1A01G041700 chr1B 16425036 16428834 3798 True 1047.666667 2610 89.6870 615 3451 3 chr1B.!!$R4 2836
3 TraesCS1A01G041700 chr1B 39846144 39846899 755 True 907.000000 907 88.7860 1843 2578 1 chr1B.!!$R3 735
4 TraesCS1A01G041700 chr7B 551897345 551898759 1414 False 880.000000 880 78.2400 1013 2434 1 chr7B.!!$F2 1421
5 TraesCS1A01G041700 chr7B 551539069 551540483 1414 False 797.000000 797 77.1690 1013 2434 1 chr7B.!!$F1 1421
6 TraesCS1A01G041700 chr7D 518089656 518091059 1403 True 848.000000 848 77.8710 1028 2437 1 chr7D.!!$R1 1409
7 TraesCS1A01G041700 chr7D 518573745 518575157 1412 False 828.000000 828 77.6160 1013 2434 1 chr7D.!!$F1 1421
8 TraesCS1A01G041700 chr7A 593014586 593015991 1405 True 839.000000 839 77.8240 1028 2437 1 chr7A.!!$R1 1409
9 TraesCS1A01G041700 chr7A 593376389 593377803 1414 False 470.500000 671 79.2595 1013 2434 2 chr7A.!!$F2 1421
10 TraesCS1A01G041700 chrUn 27691980 27692587 607 False 304.500000 468 89.7415 3 706 2 chrUn.!!$F1 703

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
125 127 1.244019 GCCTCGGCCAACAAGATTGT 61.244 55.000 2.24 0.0 37.91 2.71 F
734 900 1.468520 GGCTGACACAAATACGCATGT 59.531 47.619 0.00 0.0 0.00 3.21 F
1008 1178 0.178068 ATACCGCGTTCATGGCTTCT 59.822 50.000 4.92 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1178 0.390603 CAACGAATGCCGGTAGTGGA 60.391 55.000 9.21 0.0 43.93 4.02 R
2100 2294 1.064389 GGCCTTCTTTACCAGCTCCAT 60.064 52.381 0.00 0.0 0.00 3.41 R
2887 3234 0.108585 TGGTTCTTGCTCTGTCACCC 59.891 55.000 0.00 0.0 0.00 4.61 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 6.614694 TCCACCAACTAAATAAGTAGCTGA 57.385 37.500 0.00 0.00 37.50 4.26
125 127 1.244019 GCCTCGGCCAACAAGATTGT 61.244 55.000 2.24 0.00 37.91 2.71
163 165 4.373116 GGCAGACGCGGGAGACAA 62.373 66.667 12.47 0.00 39.92 3.18
208 210 2.234613 GCTTGCGAGCTGTGTTGTA 58.765 52.632 19.25 0.00 45.65 2.41
212 214 1.877637 TGCGAGCTGTGTTGTATGTT 58.122 45.000 0.00 0.00 0.00 2.71
221 223 5.067153 AGCTGTGTTGTATGTTTAGTTTGCA 59.933 36.000 0.00 0.00 0.00 4.08
281 283 9.607988 TTATCTTTCTAAACAATATCCGCAAGA 57.392 29.630 0.00 0.00 43.02 3.02
310 314 4.891168 TGTTAGTTTCCCTTCTTTTGGGTC 59.109 41.667 0.00 0.00 44.84 4.46
313 317 2.265589 TTCCCTTCTTTTGGGTCGAC 57.734 50.000 7.13 7.13 44.84 4.20
319 323 3.630312 CCTTCTTTTGGGTCGACTTTCAA 59.370 43.478 16.46 14.20 0.00 2.69
323 327 6.215495 TCTTTTGGGTCGACTTTCAATTTT 57.785 33.333 16.46 0.00 0.00 1.82
352 356 7.833682 TGGAAAATATAATTGAGCAGTTCCTCA 59.166 33.333 0.00 0.00 39.94 3.86
364 368 8.862325 TGAGCAGTTCCTCAATATTCTAAAAA 57.138 30.769 0.00 0.00 38.81 1.94
398 402 9.959749 TGTTCTGTTGGAAAATTATTTGTCTAC 57.040 29.630 0.00 0.00 35.51 2.59
463 468 8.731605 CCAAGTTTTTCTTAAAGAGGTAGGATC 58.268 37.037 0.00 0.00 34.66 3.36
590 597 3.250744 TCTTTTGATTACTCGCGGTCTG 58.749 45.455 6.13 0.00 0.00 3.51
610 617 1.692411 GCTCACCCCTTTGACACTTT 58.308 50.000 0.00 0.00 0.00 2.66
611 618 2.031870 GCTCACCCCTTTGACACTTTT 58.968 47.619 0.00 0.00 0.00 2.27
671 678 6.449635 TGTGCTCAACAAAAGACTACAAAT 57.550 33.333 0.00 0.00 35.24 2.32
734 900 1.468520 GGCTGACACAAATACGCATGT 59.531 47.619 0.00 0.00 0.00 3.21
736 902 3.242413 GGCTGACACAAATACGCATGTAG 60.242 47.826 0.00 0.00 33.17 2.74
737 903 3.785505 GCTGACACAAATACGCATGTAGC 60.786 47.826 0.00 0.00 40.87 3.58
738 904 3.330267 TGACACAAATACGCATGTAGCA 58.670 40.909 0.00 0.00 46.13 3.49
948 1118 2.735444 CGTCTAGTCAACGGCACATCAT 60.735 50.000 0.00 0.00 36.51 2.45
1008 1178 0.178068 ATACCGCGTTCATGGCTTCT 59.822 50.000 4.92 0.00 0.00 2.85
1392 1562 1.853319 CGAGCAGTTCGTGTTGGAC 59.147 57.895 0.00 0.00 44.27 4.02
1586 1774 2.091166 TGGAGGCTTCATATTTGGGCAT 60.091 45.455 0.00 0.00 0.00 4.40
2047 2241 1.137404 GGAACGCGTTCGCCTACTA 59.863 57.895 37.23 0.00 40.37 1.82
2258 2452 3.292936 AAGAGCGTCGACGTGGGT 61.293 61.111 35.48 19.79 42.22 4.51
2716 2989 3.381272 CACAACAGGGCTGTAATTATGGG 59.619 47.826 0.00 0.00 44.13 4.00
2855 3202 0.616111 ACGGGAGAGATGTCTTGCCT 60.616 55.000 0.00 0.00 30.97 4.75
2858 3205 1.406614 GGGAGAGATGTCTTGCCTGTG 60.407 57.143 0.00 0.00 30.97 3.66
2859 3206 1.552337 GGAGAGATGTCTTGCCTGTGA 59.448 52.381 0.00 0.00 30.97 3.58
2861 3208 3.260740 GAGAGATGTCTTGCCTGTGAAG 58.739 50.000 0.00 0.00 30.97 3.02
2862 3209 1.736681 GAGATGTCTTGCCTGTGAAGC 59.263 52.381 0.00 0.00 0.00 3.86
2863 3210 1.350351 AGATGTCTTGCCTGTGAAGCT 59.650 47.619 0.00 0.00 0.00 3.74
2864 3211 1.467734 GATGTCTTGCCTGTGAAGCTG 59.532 52.381 0.00 0.00 0.00 4.24
2865 3212 1.168407 TGTCTTGCCTGTGAAGCTGC 61.168 55.000 0.00 0.00 0.00 5.25
2866 3213 1.148949 TCTTGCCTGTGAAGCTGCA 59.851 52.632 1.02 0.00 0.00 4.41
2867 3214 1.168407 TCTTGCCTGTGAAGCTGCAC 61.168 55.000 18.75 18.75 39.22 4.57
2870 3217 3.664495 CCTGTGAAGCTGCACTGG 58.336 61.111 30.23 30.23 46.62 4.00
2871 3218 4.785767 CTGTGAAGCTGCACTGGA 57.214 55.556 25.34 4.74 39.49 3.86
2874 3221 0.109153 TGTGAAGCTGCACTGGATGT 59.891 50.000 25.34 0.00 39.49 3.06
2876 3223 1.610522 GTGAAGCTGCACTGGATGTTT 59.389 47.619 18.30 0.00 35.91 2.83
2877 3224 1.881973 TGAAGCTGCACTGGATGTTTC 59.118 47.619 1.02 0.00 0.00 2.78
2879 3226 1.531423 AGCTGCACTGGATGTTTCTG 58.469 50.000 1.02 0.00 0.00 3.02
2880 3227 0.109412 GCTGCACTGGATGTTTCTGC 60.109 55.000 0.00 0.00 0.00 4.26
2882 3229 1.610038 CTGCACTGGATGTTTCTGCAA 59.390 47.619 0.00 0.00 0.00 4.08
2883 3230 2.230508 CTGCACTGGATGTTTCTGCAAT 59.769 45.455 0.00 0.00 0.00 3.56
2884 3231 2.029739 TGCACTGGATGTTTCTGCAATG 60.030 45.455 0.00 0.00 0.00 2.82
2885 3232 2.229543 GCACTGGATGTTTCTGCAATGA 59.770 45.455 0.00 0.00 0.00 2.57
2887 3234 4.421058 CACTGGATGTTTCTGCAATGATG 58.579 43.478 0.00 0.00 0.00 3.07
2888 3235 3.446161 ACTGGATGTTTCTGCAATGATGG 59.554 43.478 0.00 0.00 0.00 3.51
2889 3236 2.761767 TGGATGTTTCTGCAATGATGGG 59.238 45.455 0.00 0.00 0.00 4.00
2891 3238 3.429822 GGATGTTTCTGCAATGATGGGTG 60.430 47.826 0.00 0.00 0.00 4.61
2892 3239 2.874014 TGTTTCTGCAATGATGGGTGA 58.126 42.857 0.00 0.00 0.00 4.02
2893 3240 2.557924 TGTTTCTGCAATGATGGGTGAC 59.442 45.455 0.00 0.00 0.00 3.67
2895 3242 2.118313 TCTGCAATGATGGGTGACAG 57.882 50.000 0.00 0.00 0.00 3.51
2897 3244 2.014857 CTGCAATGATGGGTGACAGAG 58.985 52.381 0.00 0.00 0.00 3.35
2898 3245 0.737219 GCAATGATGGGTGACAGAGC 59.263 55.000 0.00 0.00 0.00 4.09
2899 3246 1.951895 GCAATGATGGGTGACAGAGCA 60.952 52.381 0.00 0.00 0.00 4.26
2900 3247 2.439409 CAATGATGGGTGACAGAGCAA 58.561 47.619 0.00 0.00 0.00 3.91
3315 4382 3.061322 TGCAGCATTCAAATTGAAGCAC 58.939 40.909 22.33 16.90 40.05 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 127 4.949856 GCCTCTTCATATTTCTGGTTGGAA 59.050 41.667 0.00 0.00 0.00 3.53
163 165 1.350310 ACCCACAGTTTCCCCTTCGT 61.350 55.000 0.00 0.00 0.00 3.85
281 283 1.869132 GAAGGGAAACTAACAACGCGT 59.131 47.619 5.58 5.58 0.00 6.01
364 368 7.994425 AATTTTCCAACAGAACAAAAGGTTT 57.006 28.000 0.00 0.00 40.63 3.27
452 457 6.012069 TCAGACATGCTATAGATCCTACCTCT 60.012 42.308 3.21 0.00 0.00 3.69
532 538 4.288626 TGATCTACAAAGCTGTAAACCCCT 59.711 41.667 0.00 0.00 37.58 4.79
585 592 1.303643 CAAAGGGGTGAGCCAGACC 60.304 63.158 1.97 0.00 36.17 3.85
590 597 0.178990 AAGTGTCAAAGGGGTGAGCC 60.179 55.000 0.00 0.00 0.00 4.70
600 607 9.906660 CATAAACTGGCTATTAAAAGTGTCAAA 57.093 29.630 0.00 0.00 0.00 2.69
737 903 5.545658 AGAATATACCGTTGCAGTTGTTG 57.454 39.130 0.00 0.00 0.00 3.33
738 904 4.328983 CGAGAATATACCGTTGCAGTTGTT 59.671 41.667 0.00 0.00 0.00 2.83
747 913 6.072893 ACAAAACAAAGCGAGAATATACCGTT 60.073 34.615 0.00 0.00 0.00 4.44
948 1118 3.138304 AGAGAACTTGTATGCGTTGCAA 58.862 40.909 0.00 0.00 43.62 4.08
1008 1178 0.390603 CAACGAATGCCGGTAGTGGA 60.391 55.000 9.21 0.00 43.93 4.02
1386 1556 3.343421 GTGGCCGTGTCGTCCAAC 61.343 66.667 0.00 0.00 0.00 3.77
1392 1562 4.920112 TTGGTGGTGGCCGTGTCG 62.920 66.667 0.00 0.00 0.00 4.35
2100 2294 1.064389 GGCCTTCTTTACCAGCTCCAT 60.064 52.381 0.00 0.00 0.00 3.41
2855 3202 0.109153 ACATCCAGTGCAGCTTCACA 59.891 50.000 18.79 0.00 39.35 3.58
2858 3205 2.095364 CAGAAACATCCAGTGCAGCTTC 60.095 50.000 0.00 0.00 0.00 3.86
2859 3206 1.884579 CAGAAACATCCAGTGCAGCTT 59.115 47.619 0.00 0.00 0.00 3.74
2861 3208 0.109412 GCAGAAACATCCAGTGCAGC 60.109 55.000 0.00 0.00 34.18 5.25
2862 3209 1.241165 TGCAGAAACATCCAGTGCAG 58.759 50.000 0.00 0.00 39.17 4.41
2863 3210 1.689984 TTGCAGAAACATCCAGTGCA 58.310 45.000 0.00 0.00 42.24 4.57
2864 3211 2.229543 TCATTGCAGAAACATCCAGTGC 59.770 45.455 0.00 0.00 34.62 4.40
2865 3212 4.421058 CATCATTGCAGAAACATCCAGTG 58.579 43.478 0.00 0.00 0.00 3.66
2866 3213 3.446161 CCATCATTGCAGAAACATCCAGT 59.554 43.478 0.00 0.00 0.00 4.00
2867 3214 3.181479 CCCATCATTGCAGAAACATCCAG 60.181 47.826 0.00 0.00 0.00 3.86
2870 3217 3.444742 TCACCCATCATTGCAGAAACATC 59.555 43.478 0.00 0.00 0.00 3.06
2871 3218 3.194116 GTCACCCATCATTGCAGAAACAT 59.806 43.478 0.00 0.00 0.00 2.71
2874 3221 2.821378 CTGTCACCCATCATTGCAGAAA 59.179 45.455 0.00 0.00 0.00 2.52
2876 3223 1.629861 TCTGTCACCCATCATTGCAGA 59.370 47.619 0.00 0.00 0.00 4.26
2877 3224 2.014857 CTCTGTCACCCATCATTGCAG 58.985 52.381 0.00 0.00 0.00 4.41
2879 3226 0.737219 GCTCTGTCACCCATCATTGC 59.263 55.000 0.00 0.00 0.00 3.56
2880 3227 2.118313 TGCTCTGTCACCCATCATTG 57.882 50.000 0.00 0.00 0.00 2.82
2882 3229 1.911357 TCTTGCTCTGTCACCCATCAT 59.089 47.619 0.00 0.00 0.00 2.45
2883 3230 1.351076 TCTTGCTCTGTCACCCATCA 58.649 50.000 0.00 0.00 0.00 3.07
2884 3231 2.079925 GTTCTTGCTCTGTCACCCATC 58.920 52.381 0.00 0.00 0.00 3.51
2885 3232 1.271597 GGTTCTTGCTCTGTCACCCAT 60.272 52.381 0.00 0.00 0.00 4.00
2887 3234 0.108585 TGGTTCTTGCTCTGTCACCC 59.891 55.000 0.00 0.00 0.00 4.61
2888 3235 1.604278 GTTGGTTCTTGCTCTGTCACC 59.396 52.381 0.00 0.00 0.00 4.02
2889 3236 2.288666 TGTTGGTTCTTGCTCTGTCAC 58.711 47.619 0.00 0.00 0.00 3.67
2891 3238 5.645497 AGAATATGTTGGTTCTTGCTCTGTC 59.355 40.000 0.00 0.00 30.84 3.51
2892 3239 5.564550 AGAATATGTTGGTTCTTGCTCTGT 58.435 37.500 0.00 0.00 30.84 3.41
2893 3240 5.879223 AGAGAATATGTTGGTTCTTGCTCTG 59.121 40.000 0.00 0.00 34.97 3.35
2895 3242 6.749923 AAGAGAATATGTTGGTTCTTGCTC 57.250 37.500 0.00 0.00 34.97 4.26
2897 3244 9.860898 AATAAAAGAGAATATGTTGGTTCTTGC 57.139 29.630 0.00 0.00 34.97 4.01
2900 3247 8.470002 GCCAATAAAAGAGAATATGTTGGTTCT 58.530 33.333 0.00 0.00 37.69 3.01
3165 4232 2.367567 GGTAGTATTGGGCCTCATTCGA 59.632 50.000 4.53 0.00 0.00 3.71


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.